Re: [AMBER] checkpoint on Amber within batch job

From: James Maier <>
Date: Thu, 23 Jan 2014 09:54:47 -0500

On Thu, Jan 23, 2014 at 8:57 AM, Zhuang, Yu <> wrote:

> Does this means I just need to re-format the sander command for the next
> run without modification of .in file?

This depends on whether you are using a thermostat or barostat. Some
thermostats and especially barostats can give you artifacts if you restart
too quickly with the same random seed (ig flag). Setting ig differently
for each restart helps alleviate that. But if you're running say, 20 ns at
a time, it might not be a big deal.


Since you are using slurm, you may want to check out the --dependency flag
(see man sbatch)
AMBER mailing list
Received on Thu Jan 23 2014 - 07:00:04 PST
Custom Search